The Harbor Defense museum contains artifacts and exhibits that explain the history of the fort and its role in the defense of New York from invaders. The museum is located in the caponier of the old fort on the grounds of the United States Army Garrison at Fort Hamilton, Brooklyn, NY, adjacent to the base of the Verrazano Bridge.  Built between 1825-1831, the fort and the caponier have been added to the National Register of Historic Places. The fort underwent several structural modifications in the 20th century as advances in weaponry required the upgrading of its defenses and urban progress crowded its position.  Fortunately, the land side of the fort still retains much of its original character and the caponier (a miniature fort guarding the main fort's gate) is virtually untouched.

The museum office has an extensive research library on local and military history, which is open by appointment..

The permanent collections include: United States Army uniforms, accoutrements and equipment, edged weapons, small arms, cannon and munitions from 1800 to present; models, dioramas and miniatures of New York soldiers through history; artifacts relating to Fort Hamilton, the defense of New York City and the Coast Artillery, and military themed fine art.